About how to use the template to create the connectome

Hello!mrtrix experts
According to the instruction, I had used the following command to process the label convert and create the connectome which is based on the template of FreeSurfer, but i do not know how to create the connectome based on template AAL90. in this case, how should i change the command to create the connectome based on template AAL90

labelconvert sub-CON02_recon/mri/aparc+aseg.mgz $FREESURFER_HOME/ FreeSurferColorLUT.txt /usr/local/mrtrix3/share/mrtrix3/labelconvert/fs_default.txt sub- CON02_parcels.mif

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Hi Ruili,

Whether or not you will need to run the labelconvert step for the AAL parcellation will depend on where you acquired that parcellation from. I’ve seen some copies of those data where the parcel labels already increment sequentially from 1, and so no such conversion is required prior to connectome construction. If this is not the case, then it is a matter of choosing the right input LUT (which should be provided alongside the parcellation image from wherever you acquired it) and the desired output LUT. This file may well work straight away. If not, you need to look at the labelconvert documentation page to see how this command works, and therefore what data it needs to be provided with.


Hello Rob,

Thanks for your detailed clarification on how labelconvert works on the documentation page. it was really heplful.

However, i do have a follow up question.
I downloaded the AAL atlas from this link: https://www.oxcns.org/aal3.html, and as you mentioned in previous threads, it came with the “ROI_MNI_V4.txt” file which is the LUT for the atlas.

With the sample aparc+aseg.mgz/FreeSurferColorLUT, i was able to reproduce this image using “labelconvert”.

Becuase the AAL atlas doesn’t increase sequentially from 1, i also did the same thing using the labelconvert (command but i got this empty mif image below. Please any thoughts on a step i must have missed? Thanks.

When you ran labelconvert, what files did you use as the input and target lookup tables? The operation of that command depends on matching of node names between the input and target lookup tables; so if the target file doesn’t contain any of the nodes that the input file does, you’ll end up with an empty image.

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